diff --git a/.gitignore b/.gitignore
index bb28673b34bc3a64e034c30c37668ad3ba342825..27d6ff1faa1f0120c4d5adca9b748f381149feb2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,3 +9,4 @@ project/
/.project
/.settings/
dependency-reduced-pom.xml
+logs/
diff --git a/docker/config/application.tmpl b/docker/config/application.tmpl
index e34a00c0c2d4b693fc1a4ff26d3f709b43223299..6174fb409d967a2c67b5013ecc435a72fd763929 100644
--- a/docker/config/application.tmpl
+++ b/docker/config/application.tmpl
@@ -78,15 +78,15 @@ endpoints:
services:
exareme:
- miningExaremeUrl: {{ default .Env.EXAREME_URL "http://localhost:9090" }}/mining/query
+ queryExaremeUrl: {{ default .Env.EXAREME_URL "http://localhost:9090" }}/mining/query
algorithmsUrl: {{ default .Env.EXAREME_URL "http://localhost:9090" }}/mining/algorithms.json
- workflows:
- workflowUrl: {{ default .Env.WORKFLOW_URL "http://localhost:9090" }}
- jwtSecret: {{ default .Env.JWT_SECRET "secret" }}
- workflowAuthorization: {{ default .Env.WORKFLOW_AUTHORIZATION "undefined" }}
+
galaxy:
+ galaxyUrl: {{ default .Env.GALAXY_URL "http://localhost:8090/" }}
+ galaxyContext: {{ default .Env.GALAXY_CONTEXT "nativeGalaxy/workflows/list" }}
+ galaxyApiKey: {{ .Env.GALAXY_API_KEY }}
galaxyUsername: {{ default .Env.GALAXY_USERNAME "admin" }}
galaxyPassword: {{ default .Env.GALAXY_PASSWORD "password" }}
- galaxyContext: {{ default .Env.GALAXY_CONTEXT "nativeGalaxy" }}
+
keycloak:
keycloakUrl: {{ .Env.KEYCLOAK_URL }}
diff --git a/pom.xml b/pom.xml
index 674ec19543bfb73623cdf88324f209ae513aa0c3..fb47d331018bbd301afd6350b5136c2f5f2020e5 100644
--- a/pom.xml
+++ b/pom.xml
@@ -42,7 +42,7 @@
<swagger2markup-maven-plugin.version>1.0.0</swagger2markup-maven-plugin.version>
<maven-compiler-plugin.version>3.5.1</maven-compiler-plugin.version>
<hibernate4-maven-plugin.version>1.1.1</hibernate4-maven-plugin.version>
- <flyway-core.version>4.0.3</flyway-core.version>
+ <flyway-core.version>4.2.0</flyway-core.version>
<hibernate-jpa-2.1-api.version>1.0.0.Final</hibernate-jpa-2.1-api.version>
<hibernate.version>4.3.11.Final</hibernate.version>
<spring-data-jpa.version>1.10.11.RELEASE</spring-data-jpa.version>
@@ -218,6 +218,34 @@
<artifactId>java-jwt</artifactId>
<version>3.8.3</version>
</dependency>
+
+ <!-- https://mvnrepository.com/artifact/com.github.jmchilton.blend4j/blend4j -->
+ <dependency>
+ <groupId>com.github.jmchilton.blend4j</groupId>
+ <artifactId>blend4j</artifactId>
+ <version>0.2.0</version>
+ </dependency>
+
+ <dependency>
+ <groupId>com.squareup.retrofit2</groupId>
+ <artifactId>retrofit</artifactId>
+ <version>2.5.0</version>
+ </dependency>
+
+ <!-- https://mvnrepository.com/artifact/com.squareup.retrofit2/converter-gson -->
+ <dependency>
+ <groupId>com.squareup.retrofit2</groupId>
+ <artifactId>converter-gson</artifactId>
+ <version>2.4.0</version>
+ </dependency>
+
+ <!-- https://mvnrepository.com/artifact/com.squareup.okhttp3/logging-interceptor -->
+ <dependency>
+ <groupId>com.squareup.okhttp3</groupId>
+ <artifactId>logging-interceptor</artifactId>
+ <version>3.12.1</version>
+ </dependency>
+
<dependency>
<groupId>com.auth0</groupId>
<artifactId>java-jwt</artifactId>
diff --git a/src/main/java/eu/hbp/mip/MIPApplication.java b/src/main/java/eu/hbp/mip/MIPApplication.java
index befb16ec91ee35a0bbd2c9a7631f30be9cde4b21..e6ccd8e1e2d1e71107a9d262b21e02bb070eefae 100644
--- a/src/main/java/eu/hbp/mip/MIPApplication.java
+++ b/src/main/java/eu/hbp/mip/MIPApplication.java
@@ -9,7 +9,6 @@ import org.springframework.boot.SpringApplication;
import org.springframework.boot.autoconfigure.SpringBootApplication;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.annotation.Value;
@SpringBootApplication
public class MIPApplication {
diff --git a/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java b/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
index 5c03ec4ebf5a95f424e4214de582c7967ce14d93..6b973dc6575c2027a344b0a872591f1b465e9a87 100644
--- a/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
+++ b/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
@@ -46,5 +46,4 @@ public class PersistenceConfiguration {
flyway.setDataSource(portalDataSource());
return flyway;
}
-
}
diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
new file mode 100644
index 0000000000000000000000000000000000000000..efe69c07207cd1b247b20cc9a953a37cb8bea7b5
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
@@ -0,0 +1,157 @@
+package eu.hbp.mip.controllers;
+
+import com.github.jmchilton.blend4j.galaxy.GalaxyInstance;
+import com.github.jmchilton.blend4j.galaxy.GalaxyInstanceFactory;
+import com.github.jmchilton.blend4j.galaxy.WorkflowsClient;
+import com.github.jmchilton.blend4j.galaxy.beans.Workflow;
+import com.google.gson.Gson;
+import eu.hbp.mip.controllers.galaxy.retrofit.RetroFitGalaxyClients;
+import eu.hbp.mip.controllers.galaxy.retrofit.RetrofitClientInstance;
+import eu.hbp.mip.model.AlgorithmDTO;
+import eu.hbp.mip.model.galaxy.WorkflowDTO;
+import eu.hbp.mip.utils.HTTPUtil;
+import eu.hbp.mip.utils.UserActionLogging;
+import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiOperation;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RestController;
+import retrofit2.Call;
+import retrofit2.Response;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.LinkedList;
+import java.util.List;
+
+import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
+
+@RestController
+@RequestMapping(value = "/algorithms", produces = {APPLICATION_JSON_VALUE})
+@Api(value = "/algorithms")
+public class AlgorithmsApi {
+
+ private static final Gson gson = new Gson();
+
+ @Value("#{'${services.exareme.algorithmsUrl}'}")
+ private String exaremeAlgorithmsUrl;
+
+ @Value("#{'${services.galaxy.galaxyUrl}'}")
+ private String galaxyUrl;
+
+ @Value("#{'${services.galaxy.galaxyApiKey}'}")
+ private String galaxyApiKey;
+
+ @ApiOperation(value = "List all algorithms", response = String.class)
+ @RequestMapping(method = RequestMethod.GET)
+ public ResponseEntity<List<AlgorithmDTO>> getAlgorithms() {
+ UserActionLogging.LogAction("List all algorithms", "");
+
+ List<AlgorithmDTO> exaremeAlgorithms = getExaremeAlgorithms();
+ List<AlgorithmDTO> galaxyAlgorithms = getGalaxyWorkflows();
+
+ List<AlgorithmDTO> algorithms = new LinkedList<>();
+ if (exaremeAlgorithms != null) {
+ algorithms.addAll(exaremeAlgorithms);
+ } else {
+ UserActionLogging.LogAction("List all algorithms",
+ "Getting exareme algorithms failed and returned null");
+ }
+ if (galaxyAlgorithms != null) {
+ algorithms.addAll(galaxyAlgorithms);
+ } else {
+ UserActionLogging.LogAction("List all algorithms",
+ "Getting galaxy workflows failed and returned null");
+ }
+
+ return ResponseEntity.ok(algorithms);
+ }
+
+ /**
+ * This method gets all the available exareme algorithms and
+ *
+ * @return a list of AlgorithmDTOs or null if something fails
+ */
+ public List<AlgorithmDTO> getExaremeAlgorithms() {
+ UserActionLogging.LogAction("List exareme algorithms", "");
+
+ List<AlgorithmDTO> algorithms = new LinkedList<>();
+ // Get exareme algorithms
+ try {
+ StringBuilder response = new StringBuilder();
+ HTTPUtil.sendGet(exaremeAlgorithmsUrl, response);
+
+ algorithms = gson.fromJson(response.toString(), algorithms.getClass());
+ } catch (IOException e) {
+ UserActionLogging.LogAction("List exareme algorithms", "An exception occurred: " + e.getMessage());
+ return null;
+ }
+
+ UserActionLogging.LogAction("List exareme algorithms",
+ "Completed, returned " + algorithms.size() + " algorithms.");
+ return algorithms;
+ }
+
+ /**
+ * This method gets all the available galaxy workflows, converts them into algorithms and
+ *
+ * @return a list of AlgorithmDTOs or null if something fails
+ */
+ public List<AlgorithmDTO> getGalaxyWorkflows() {
+ UserActionLogging.LogAction("List Galaxy workflows", "");
+
+ List<Workflow> workflowList = null;
+ try {
+ // Get all the workflows with the galaxy client
+ final GalaxyInstance instance = GalaxyInstanceFactory.get(galaxyUrl, galaxyApiKey);
+ final WorkflowsClient workflowsClient = instance.getWorkflowsClient();
+
+ workflowList = new ArrayList<>(workflowsClient.getWorkflows());
+ } catch (Exception e) {
+ UserActionLogging.LogAction("List Galaxy workflows", "Error when calling list galaxy workflows: " + e.getMessage());
+
+ return null;
+ }
+
+ // Get the workflow details with the custom client to receive them as a WorkflowDTO
+ List<WorkflowDTO> workflows = new LinkedList<>();
+ // Create the request client
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ for (Workflow workflow : workflowList) {
+ // Call Galaxy to run the workflow
+ Call<WorkflowDTO> call = service.getWorkflowFromGalaxy(workflow.getId(), galaxyApiKey);
+ try {
+ Response<WorkflowDTO> response = call.execute();
+
+ if (response.code() == 200) { // Call succeeded
+ workflows.add(response.body());
+
+ } else { // Something unexpected happened
+ String msgErr = gson.toJson(response.errorBody());
+ UserActionLogging.LogAction("List Galaxy workflows", "Error Response: " + msgErr);
+ return null;
+ }
+ } catch (Exception e) {
+ UserActionLogging.LogAction("List Galaxy workflows", "An exception occurred: " + e.getMessage());
+ return null;
+ }
+ }
+ UserActionLogging.LogAction("List Galaxy workflows", "Workflows fetched: " + workflows.size());
+
+ // Convert the workflows to algorithms
+ List<AlgorithmDTO> algorithms = new LinkedList<>();
+ for (WorkflowDTO workflow : workflows) {
+ UserActionLogging.LogAction("List Galaxy workflows", "Converting workflow: " + workflow);
+
+ algorithms.add(workflow.convertToAlgorithmDTO());
+
+ UserActionLogging.LogAction("List Galaxy workflows",
+ "Converted algorithm: " + algorithms.get(algorithms.size() - 1));
+ }
+
+ UserActionLogging.LogAction("List Galaxy workflows", "Completed!");
+ return algorithms;
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java b/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java
deleted file mode 100644
index 897828faff819f71c108bbde751598b6b494776f..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java
+++ /dev/null
@@ -1,25 +0,0 @@
-/*
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.controllers;
-
-import io.swagger.annotations.*;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RestController;
-
-
-import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
-
-
-@RestController
-@RequestMapping(value = "/datasets", produces = {APPLICATION_JSON_VALUE})
-@Api(value = "/datasets", description = "the datasets API")
-public class DatasetsApi {
-
- private static final Logger LOGGER = LoggerFactory.getLogger(DatasetsApi.class);
-
-
-}
diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
index deef20f755c0fd961e09a238eb662a671a9532e2..f876e315ed224bfc667b6ff6fb9337a2bafb361f 100644
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
@@ -1,48 +1,60 @@
package eu.hbp.mip.controllers;
-import com.google.gson.*;
+import com.github.jmchilton.blend4j.galaxy.GalaxyInstance;
+import com.github.jmchilton.blend4j.galaxy.GalaxyInstanceFactory;
+import com.github.jmchilton.blend4j.galaxy.WorkflowsClient;
+import com.github.jmchilton.blend4j.galaxy.beans.Workflow;
+import com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails;
+import com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputDefinition;
import com.google.common.collect.Lists;
-import com.google.gson.Gson;
-import com.google.gson.GsonBuilder;
-
+import com.google.gson.*;
+import eu.hbp.mip.controllers.galaxy.retrofit.RetroFitGalaxyClients;
+import eu.hbp.mip.controllers.galaxy.retrofit.RetrofitClientInstance;
import eu.hbp.mip.model.*;
+import eu.hbp.mip.model.ExperimentExecutionDTO.AlgorithmExecutionDTO.AlgorithmExecutionParamDTO;
+import eu.hbp.mip.model.galaxy.ErrorResponse;
+import eu.hbp.mip.model.galaxy.GalaxyWorkflowResult;
+import eu.hbp.mip.model.galaxy.PostWorkflowToGalaxyDtoResponse;
import eu.hbp.mip.repositories.ExperimentRepository;
import eu.hbp.mip.repositories.ModelRepository;
import eu.hbp.mip.utils.HTTPUtil;
+import eu.hbp.mip.utils.UserActionLogging;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import io.swagger.annotations.ApiParam;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
+import org.codehaus.jettison.json.JSONException;
+import org.codehaus.jettison.json.JSONObject;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.*;
-import eu.hbp.mip.utils.JWTUtil;
-import eu.hbp.mip.utils.UserActionLogging;
+import retrofit2.Call;
+import retrofit2.Response;
import java.io.IOException;
import java.util.*;
+
+import static java.lang.Thread.sleep;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
-/**
- * Created by habfast on 21/04/16.
+/*
+ This api is creating experiments and running it's algorithm on the
+ exareme or galaxy clients.
*/
+
@RestController
-@RequestMapping(value = "/experiments", produces = { APPLICATION_JSON_VALUE })
-@Api(value = "/experiments", description = "the experiments API")
+@RequestMapping(value = "/experiments", produces = {APPLICATION_JSON_VALUE})
+@Api(value = "/experiments")
public class ExperimentApi {
- //private static final Logger LOGGER = LoggerFactory.getLogger(ExperimentApi.class);
-
private static final Gson gson = new Gson();
private static final Gson gsonOnlyExposed = new GsonBuilder().serializeNulls()
.setDateFormat("yyyy-MM-dd'T'HH:mm:ssZ").excludeFieldsWithoutExposeAnnotation().create();
- @Value("#{'${services.exareme.miningExaremeUrl:http://localhost:9090/mining/query}'}")
- public String miningExaremeQueryUrl;
+ @Value("#{'${services.exareme.queryExaremeUrl}'}")
+ private String queryExaremeUrl;
@Value("#{'${services.workflows.workflowUrl}'}")
private String workflowUrl;
@@ -50,6 +62,12 @@ public class ExperimentApi {
@Value("#{'${services.workflows.jwtSecret}'}")
private String jwtSecret;
+ @Value("#{'${services.galaxy.galaxyUrl}'}")
+ private String galaxyUrl;
+
+ @Value("#{'${services.galaxy.galaxyApiKey}'}")
+ private String galaxyApiKey;
+
@Autowired
private UserInfo userInfo;
@@ -59,94 +77,6 @@ public class ExperimentApi {
@Autowired
private ExperimentRepository experimentRepository;
- @ApiOperation(value = "Create an experiment on Exareme", response = Experiment.class)
- @RequestMapping(value = "/exareme", method = RequestMethod.POST)
- public ResponseEntity<String> runExaremeExperiment(@RequestBody ExperimentQuery expQuery) {
- //LOGGER.info("send ExaremeExperiment");
-
- Experiment experiment = saveExperiment(expQuery);
-
- String algoCode = expQuery.getAlgorithms().get(0).getCode();
- List<AlgorithmParam> params = expQuery.getAlgorithms().get(0).getParameters();
- new Thread(() -> {
- List<HashMap<String, String>> queryList = new ArrayList<HashMap<String, String>>();
-
- if (params != null) {
- for (AlgorithmParam p : params) {
- queryList.add(makeObject(p.getName(), p.getValue()));
- }
- }
-
- String query = gson.toJson(queryList);
- String url = miningExaremeQueryUrl + "/" + algoCode;
-
- // Results are stored in the experiment object
- try {
- StringBuilder results = new StringBuilder();
- int code = HTTPUtil.sendPost(url, query, results);
- experiment.setResult("[" + results.toString() + "]");
- experiment.setHasError(code >= 400);
- experiment.setHasServerError(code >= 500);
- } catch (IOException e) {
- //LOGGER.trace("Invalid UUID", e);
- //LOGGER.warn("Exareme experiment failed to run properly !");
- experiment.setHasError(true);
- experiment.setHasServerError(true);
- experiment.setResult(e.getMessage());
- }
- finishExperiment(experiment);
- }).start();
-
- UserActionLogging.LogAction("create ExaremeExperiment", "no info");
-
- return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
- }
-
- @ApiOperation(value = "Create a workflow", response = Experiment.class)
- @RequestMapping(value = "/workflow", method = RequestMethod.POST)
- public ResponseEntity<String> runWorkflow(@RequestBody ExperimentQuery expQuery) {
-
- Experiment experiment = saveExperiment(expQuery);
-
- String algoCode = expQuery.getAlgorithms().get(0).getCode();
- List<AlgorithmParam> params = expQuery.getAlgorithms().get(0).getParameters();
-
- User user = userInfo.getUser();
- String token = JWTUtil.getJWT(jwtSecret, user.getEmail());
-
- HashMap<String, String> queryMap = new HashMap<String, String>();
-
- if (params != null) {
- for (AlgorithmParam p : params) {
- queryMap.put(p.getName(), p.getValue());
- }
- }
-
- String query = gson.toJson(queryMap);
- String url = workflowUrl + "/runWorkflow/" + algoCode;
- // Results are stored in the experiment object
-
- new Thread(() -> {
- try {
- StringBuilder results = new StringBuilder();
- int code = HTTPUtil.sendAuthorizedHTTP(url, query, results, "POST", "Bearer " + token);
- experiment.setResult("[" + results.toString() + "]");
- experiment.setHasError(code >= 400);
- experiment.setHasServerError(code >= 500);
- } catch (IOException e) {
- //LOGGER.trace("Invalid UUID", e);
- experiment.setHasError(true);
- experiment.setHasServerError(true);
- experiment.setResult(e.getMessage());
- }
- finishExperiment(experiment);
- }).start();
-
- UserActionLogging.LogAction("create workflow", "no info");
-
- return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
- }
-
@ApiOperation(value = "get an experiment", response = Experiment.class)
@RequestMapping(value = "/{uuid}", method = RequestMethod.GET)
public ResponseEntity<String> getExperiment(
@@ -157,8 +87,7 @@ public class ExperimentApi {
try {
experimentUuid = UUID.fromString(uuid);
} catch (IllegalArgumentException iae) {
- //LOGGER.trace("Invalid UUID", iae);
- //LOGGER.warn("An invalid Experiment UUID was received ! " + uuid);
+ UserActionLogging.LogAction("Get Experiment", "Invalid Experiment UUID.");
return ResponseEntity.badRequest().body("Invalid Experiment UUID");
}
@@ -167,95 +96,24 @@ public class ExperimentApi {
if (experiment == null) {
return new ResponseEntity<>("Not found", HttpStatus.NOT_FOUND);
}
-
- UserActionLogging.LogAction("Get an experiment ", " uuid : "+ uuid);
-
- return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
- }
-
- @ApiOperation(value = "get workflow status", response = String.class)
- @RequestMapping(value = "/workflow/status/{historyId}", method = RequestMethod.GET)
- public ResponseEntity<String> getWorkflowStatus(
- @ApiParam(value = "historyId", required = true) @PathVariable("historyId") String historyId) {
-
- UserActionLogging.LogAction("Get a workflow status", " historyId : "+ historyId);
-
- String url = workflowUrl + "/getWorkflowStatus/" + historyId;
- try {
- User user = userInfo.getUser();
- String token = JWTUtil.getJWT(jwtSecret, user.getEmail());
- StringBuilder response = new StringBuilder();
- HTTPUtil.sendAuthorizedHTTP(url, "", response, "GET", "Bearer " + token);
- JsonElement element = new JsonParser().parse(response.toString());
-
- return ResponseEntity.ok(gson.toJson(element));
- } catch (IOException e) {
- return ResponseEntity.status(500).body(e.getMessage());
- }
-
- }
-
- // TODO: factorize workflow results
- @ApiOperation(value = "get workflow results", response = String.class)
- @RequestMapping(value = "/workflow/results/{historyId}", method = RequestMethod.GET)
- public ResponseEntity<String> getWorkflowResults(
- @ApiParam(value = "historyId", required = true) @PathVariable("historyId") String historyId) {
- UserActionLogging.LogAction("Get workflow results", " historyId : "+ historyId);
-
- String url = workflowUrl + "/getWorkflowResults/" + historyId;
- try {
- StringBuilder response = new StringBuilder();
- User user = userInfo.getUser();
- String token = JWTUtil.getJWT(jwtSecret, user.getEmail());
- HTTPUtil.sendAuthorizedHTTP(url, "", response, "GET", "Bearer " + token);
- JsonElement element = new JsonParser().parse(response.toString());
-
- return ResponseEntity.ok(gson.toJson(element));
- } catch (IOException e) {
- return ResponseEntity.status(500).body(e.getMessage());
- }
- }
- @ApiOperation(value = "get workflow result body", response = String.class)
- @RequestMapping(value = "/workflow/resultsbody/{historyId}/content/{resultId}", method = RequestMethod.GET)
- public ResponseEntity<String> getWorkflowResultBody(
- @ApiParam(value = "historyId", required = true) @PathVariable("historyId") String historyId,
- @ApiParam(value = "resultId", required = true) @PathVariable("resultId") String resultId) {
-
- UserActionLogging.LogAction("Get workflow result content", " historyId : "+ historyId + " resultId : "+ resultId);
-
- String url = workflowUrl + "/getWorkflowResultsBody/" + historyId + "/contents/" + resultId;
- try {
- StringBuilder response = new StringBuilder();
- User user = userInfo.getUser();
- String token = JWTUtil.getJWT(jwtSecret, user.getEmail());
- HTTPUtil.sendAuthorizedHTTP(url, "", response, "GET", "Bearer " + token);
- JsonElement element = new JsonParser().parse(response.toString());
+ UserActionLogging.LogAction("Get an experiment ", " uuid : " + uuid);
- return ResponseEntity.ok(gson.toJson(element));
- } catch (IOException e) {
- return ResponseEntity.status(500).body(e.getMessage());
- }
+ return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
}
- @ApiOperation(value = "get workflow result details", response = String.class)
- @RequestMapping(value = "/workflow/resultsdetails/{historyId}/content/{resultId}", method = RequestMethod.GET)
- public ResponseEntity<String> getWorkflowResultsDetails(
- @ApiParam(value = "historyId", required = true) @PathVariable("historyId") String historyId,
- @ApiParam(value = "resultId", required = true) @PathVariable("resultId") String resultId) {
- UserActionLogging.LogAction("Get workflow result details", " historyId : "+ historyId + " resultId : "+ resultId);
+ @ApiOperation(value = "Create an experiment", response = Experiment.class)
+ @RequestMapping(value = "/runAlgorithm", method = RequestMethod.POST)
+ public ResponseEntity<String> runExperiment(@RequestBody ExperimentExecutionDTO experimentExecutionDTO) {
+ UserActionLogging.LogAction("Run algorithm", "Running the algorithm...");
- String url = workflowUrl + "/getWorkflowResultsDetails/" + historyId + "/contents/" + resultId;
- try {
- StringBuilder response = new StringBuilder();
- User user = userInfo.getUser();
- String token = JWTUtil.getJWT(jwtSecret, user.getEmail());
- HTTPUtil.sendAuthorizedHTTP(url, "", response, "GET", "Bearer " + token);
- JsonElement element = new JsonParser().parse(response.toString());
+ // Get the type of algorithm
+ String algorithmType = experimentExecutionDTO.getAlgorithms().get(0).getType();
- return ResponseEntity.ok(gson.toJson(element));
- } catch (IOException e) {
- return ResponseEntity.status(500).body(e.getMessage());
+ if (algorithmType.equals("workflow")) {
+ return runGalaxyWorkflow(experimentExecutionDTO);
+ } else {
+ return runExaremeAlgorithm(experimentExecutionDTO);
}
}
@@ -264,7 +122,7 @@ public class ExperimentApi {
public ResponseEntity<String> markExperimentAsViewed(
@ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
- UserActionLogging.LogAction("Mark an experiment as viewed", " uuid : "+ uuid);
+ UserActionLogging.LogAction("Mark an experiment as viewed", " uuid : " + uuid);
Experiment experiment;
UUID experimentUuid;
@@ -283,7 +141,7 @@ public class ExperimentApi {
experiment.setResultsViewed(true);
experimentRepository.save(experiment);
- UserActionLogging.LogAction("Experiment updated (marked as viewed)", " ");
+ UserActionLogging.LogAction("Experiment updated (marked as viewed)", " ");
return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
}
@@ -293,8 +151,8 @@ public class ExperimentApi {
public ResponseEntity<String> markExperimentAsShared(
@ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
- UserActionLogging.LogAction("Mark an experiment as shared", " uuid : "+ uuid);
-
+ UserActionLogging.LogAction("Mark an experiment as shared", " uuid : " + uuid);
+
return doMarkExperimentAsShared(uuid, true);
}
@@ -302,27 +160,27 @@ public class ExperimentApi {
@RequestMapping(value = "/{uuid}/markAsUnshared", method = RequestMethod.GET)
public ResponseEntity<String> markExperimentAsUnshared(
@ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
- UserActionLogging.LogAction("Mark an experiment as unshared", " uuid : "+ uuid);
-
+ UserActionLogging.LogAction("Mark an experiment as unshared", " uuid : " + uuid);
+
return doMarkExperimentAsShared(uuid, false);
}
@ApiOperation(value = "list experiments", response = Experiment.class, responseContainer = "List")
- @RequestMapping(method = RequestMethod.GET, params = { "maxResultCount" })
+ @RequestMapping(method = RequestMethod.GET, params = {"maxResultCount"})
public ResponseEntity<String> listExperiments(
@ApiParam(value = "maxResultCount") @RequestParam int maxResultCount) {
- UserActionLogging.LogAction("List experiments", " maxResultCount : "+ maxResultCount);
-
+ UserActionLogging.LogAction("List experiments", " maxResultCount : " + maxResultCount);
+
return doListExperiments(false, null);
}
@ApiOperation(value = "list experiments", response = Experiment.class, responseContainer = "List")
- @RequestMapping(method = RequestMethod.GET, params = { "slug", "maxResultCount" })
+ @RequestMapping(method = RequestMethod.GET, params = {"slug", "maxResultCount"})
public ResponseEntity<String> listExperiments(@ApiParam(value = "slug") @RequestParam("slug") String modelSlug,
- @ApiParam(value = "maxResultCount") @RequestParam("maxResultCount") int maxResultCount) {
+ @ApiParam(value = "maxResultCount") @RequestParam("maxResultCount") int maxResultCount) {
- UserActionLogging.LogAction("List experiments", " modelSlug : "+ modelSlug);
+ UserActionLogging.LogAction("List experiments", " modelSlug : " + modelSlug);
if (maxResultCount <= 0 && (modelSlug == null || "".equals(modelSlug))) {
return new ResponseEntity<>("You must provide at least a slug or a limit of result",
@@ -333,9 +191,9 @@ public class ExperimentApi {
}
@ApiOperation(value = "list my experiments", response = Experiment.class, responseContainer = "List")
- @RequestMapping(method = RequestMethod.GET, params = { "mine" })
+ @RequestMapping(method = RequestMethod.GET, params = {"mine"})
public ResponseEntity<String> listMyExperiments(@ApiParam(value = "mine") @RequestParam("mine") boolean mine) {
- UserActionLogging.LogAction("List my experiments", " mine : "+ mine);
+ UserActionLogging.LogAction("List my experiments", " mine : " + mine);
return doListExperiments(true, null);
}
@@ -352,7 +210,7 @@ public class ExperimentApi {
}
if (modelSlug != null && !"".equals(modelSlug)) {
- for (Iterator<Experiment> it = expList.iterator(); it.hasNext();) {
+ for (Iterator<Experiment> it = expList.iterator(); it.hasNext(); ) {
Experiment e = it.next();
e.setResult(null);
e.setAlgorithms(null);
@@ -385,43 +243,527 @@ public class ExperimentApi {
experiment.setShared(shared);
experimentRepository.save(experiment);
-
- UserActionLogging.LogAction("Experiment updated (marked as shared)", "");
+
+ UserActionLogging.LogAction("Experiment updated (marked as shared)", "");
return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
}
+ /* ------------------------------- EXPERIMENT MODEL METHODS ----------------------------------------------------*/
+
+ public Experiment createExperiment(ExperimentExecutionDTO experimentExecutionDTO){
+ User user = userInfo.getUser();
+
+ Experiment experiment = new Experiment();
+ experiment.setUuid(UUID.randomUUID());
+ experiment.setCreatedBy(user);
+ experiment.setAlgorithms(gson.toJson(experimentExecutionDTO.getAlgorithms()));
+ Model model = modelRepository.findOne(experimentExecutionDTO.getModel());
+ experiment.setModel(model);
+ experiment.setName(experimentExecutionDTO.getName());
+ experimentRepository.save(experiment);
+
+ UserActionLogging.LogAction("Created an experiment", " id : " + experiment.getUuid());
+ UserActionLogging.LogAction("Created an experiment", " algorithms : " + experiment.getAlgorithms());
+ UserActionLogging.LogAction("Created an experiment", " model : " + experiment.getModel().getSlug());
+ UserActionLogging.LogAction("Created an experiment", " name : " + experiment.getName());
+ return experiment;
+ }
+
+ private void saveExperiment(Experiment experiment) {
+ UserActionLogging.LogAction("Saved an experiment", " id : " + experiment.getUuid());
+ UserActionLogging.LogAction("Saved an experiment", " algorithms : " + experiment.getAlgorithms());
+ UserActionLogging.LogAction("Saved an experiment", " model : " + experiment.getModel().getSlug());
+ UserActionLogging.LogAction("Saved an experiment", " name : " + experiment.getName());
+ UserActionLogging.LogAction("Saved an experiment", " historyId : " + experiment.getWorkflowHistoryId());
+ UserActionLogging.LogAction("Saved an experiment", " status : " + experiment.getWorkflowStatus());
+
+ experimentRepository.save(experiment);
+
+ UserActionLogging.LogAction("Experiment saved", "");
+ }
+
private void finishExperiment(Experiment experiment) {
experiment.setFinished(new Date());
experimentRepository.save(experiment);
- UserActionLogging.LogAction("Experiment updated (finished)","");
+ UserActionLogging.LogThreadAction("Experiment finished!", "");
}
- private HashMap<String, String> makeObject(String name, String value) {
- HashMap<String, String> o = new HashMap<String, String>();
- o.put("name", name);
- o.put("value", value);
+ /* -------------------------------------- EXAREME CALLS ---------------------------------------------------------*/
+
+ /**
+ * The runExaremeExperiment will POST the algorithm to the exareme client
+ *
+ * @param experimentExecutionDTO is the request with the experiment information
+ * @return the response to be returned
+ */
+ public ResponseEntity<String> runExaremeAlgorithm(ExperimentExecutionDTO experimentExecutionDTO) {
+ UserActionLogging.LogAction("Run exareme algorithm", "Running the algorithm...");
+
+ Experiment experiment = createExperiment(experimentExecutionDTO);
+
+ // Run the 1st algorithm from the list
+ String algorithmName = experimentExecutionDTO.getAlgorithms().get(0).getName();
+
+ // Get the parameters
+ List<ExperimentExecutionDTO.AlgorithmExecutionDTO.AlgorithmExecutionParamDTO> algorithmParameters
+ = experimentExecutionDTO.getAlgorithms().get(0).getParameters();
+
+ String body = gson.toJson(algorithmParameters);
+ String url = queryExaremeUrl + "/" + algorithmName;
+ UserActionLogging.LogAction("Run exareme algorithm", "url: " + url + ", body: " + body);
+
+ ResponseEntity<String> response = new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
+ UserActionLogging.LogAction("Run exareme algorithm",
+ "Completed, returning: " + experiment.toString());
- return o;
+ UserActionLogging.LogAction("Run exareme algorithm",
+ "Starting exareme execution thread");
+ new Thread(() -> {
+ // ATTENTION: Inside the Thread only LogThreadAction should be used, not LogAction!
+ UserActionLogging.LogThreadAction("Run exareme algorithm",
+ "Thread started!");
+
+ try {
+ UserActionLogging.LogThreadAction("Run exareme algorithm",
+ "Thread started!");
+ StringBuilder results = new StringBuilder();
+ int code = HTTPUtil.sendPost(url, body, results);
+
+ UserActionLogging.LogThreadAction("Run exareme algorithm",
+ "Algorithm finished with code: " + code);
+
+ // Results are stored in the experiment object
+ experiment.setResult("[" + results.toString() + "]");
+ experiment.setHasError(code >= 400);
+ experiment.setHasServerError(code >= 500);
+ } catch (Exception e) {
+ UserActionLogging.LogThreadAction("Run exareme algorithm",
+ "There was an exception: " + e.getMessage());
+
+ experiment.setHasError(true);
+ experiment.setHasServerError(true);
+ experiment.setResult(e.getMessage());
+ }
+ UserActionLogging.LogThreadAction("Run exareme algorithm",
+ "Finished the experiment: " + experiment.toString());
+ finishExperiment(experiment);
+
+ UserActionLogging.LogThreadAction("Run exareme algorithm",
+ "Finished!");
+ }).start();
+
+ return response;
}
- private Experiment saveExperiment(ExperimentQuery expQuery) {
+ /* --------------------------------------- GALAXY CALLS ---------------------------------------------------------*/
- Experiment experiment = new Experiment();
- experiment.setUuid(UUID.randomUUID());
- User user = userInfo.getUser();
- experiment.setAlgorithms(gson.toJson(expQuery.getAlgorithms()));
- experiment.setValidations(gson.toJson(expQuery.getValidations()));
- experiment.setName(expQuery.getName());
- experiment.setCreatedBy(user);
- experiment.setModel(modelRepository.findOne(expQuery.getModel()));
- experimentRepository.save(experiment);
+ /**
+ * The runWorkflow will POST the algorithm to the galaxy client
+ *
+ * @param experimentExecutionDTO is the request with the experiment information
+ * @return the response to be returned
+ */
+ public ResponseEntity<String> runGalaxyWorkflow(ExperimentExecutionDTO experimentExecutionDTO) {
+ UserActionLogging.LogAction("Run workflow", "Running a workflow...");
- UserActionLogging.LogAction("Saved an experiment", " id : "+experiment.getUuid());
+ Experiment experiment = createExperiment(experimentExecutionDTO);
- return experiment;
+ // Run the 1st algorithm from the list
+ String workflowId = experimentExecutionDTO.getAlgorithms().get(0).getName();
+
+ // Get the parameters
+ List<AlgorithmExecutionParamDTO> algorithmParameters
+ = experimentExecutionDTO.getAlgorithms().get(0).getParameters();
+
+ // Convert the parameters to workflow parameters
+ HashMap<String, String> algorithmParamsIncludingEmpty = new HashMap<>();
+ if (algorithmParameters != null) {
+ for (AlgorithmExecutionParamDTO param : algorithmParameters) {
+ algorithmParamsIncludingEmpty.put(param.getName(), param.getValue());
+ }
+ }
+
+ // Get all the algorithm parameters because the frontend provides only the non-null
+ final GalaxyInstance instance = GalaxyInstanceFactory.get(galaxyUrl, galaxyApiKey);
+ final WorkflowsClient workflowsClient = instance.getWorkflowsClient();
+ Workflow workflow = null;
+ for (Workflow curWorkflow : workflowsClient.getWorkflows()) {
+ if (curWorkflow.getId().equals(workflowId)) {
+ workflow = curWorkflow;
+ break;
+ }
+ }
+ if (workflow == null) {
+ UserActionLogging.LogAction("Run workflow",
+ "Could not find algorithm code: " + workflowId);
+ return ResponseEntity.status(HttpStatus.BAD_REQUEST)
+ .body(new ErrorResponse("Could not find galaxy algorithm.").toString());
+ }
+ final WorkflowDetails workflowDetails = workflowsClient.showWorkflow(workflow.getId());
+ for (Map.Entry<String, WorkflowInputDefinition> workflowParameter : workflowDetails.getInputs().entrySet()) {
+ if (!(algorithmParamsIncludingEmpty.containsKey(workflowParameter.getValue().getUuid()))) {
+ algorithmParamsIncludingEmpty.put(workflowParameter.getValue().getUuid(), "");
+ }
+ }
+
+ // Create the body of the request
+ HashMap<String, HashMap<String, String>> requestBody = new HashMap<>();
+ requestBody.put("inputs", algorithmParamsIncludingEmpty);
+ JsonObject requestBodyJson = new JsonParser().parse(gson.toJson(requestBody)).getAsJsonObject();
+
+ // Create the request client
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ UserActionLogging.LogAction("Run workflow", "Running Galaxy workflow with id: " + workflow.getId());
+
+ // Call Galaxy to run the workflow
+ Call<PostWorkflowToGalaxyDtoResponse> call = service.postWorkflowToGalaxy(workflow.getId(), galaxyApiKey, requestBodyJson);
+ try {
+ Response<PostWorkflowToGalaxyDtoResponse> response = call.execute();
+
+ if (response.code() == 200) { // Call succeeded
+ String responseBody = gson.toJson(response.body());
+ UserActionLogging.LogAction("Run workflow", "Response: " + responseBody);
+
+ String historyId = (String) new JSONObject(responseBody).get("history_id");
+ experiment.setWorkflowHistoryId(historyId);
+ experiment.setWorkflowStatus("running");
+ experiment.setHasError(false);
+ experiment.setHasServerError(response.code() >= 500);
+
+ } else { // Something unexpected happened
+ String msgErr = gson.toJson(response.errorBody());
+ UserActionLogging.LogAction("Run workflow", "Error Response: " + msgErr);
+
+ // Values are read from streams.
+ JSONObject jObjectError = new JSONObject(msgErr);
+ String errMsg = jObjectError.get("err_msg").toString();
+
+ experiment.setResult("[" + new ErrorResponse(errMsg).toString() + "]");
+ experiment.setHasError(response.code() >= 400);
+ experiment.setHasServerError(response.code() >= 500);
+ }
+
+ } catch (Exception e) {
+ UserActionLogging.LogAction("Run workflow", "An exception occurred: " + e.getMessage());
+ experiment.setHasError(true);
+ experiment.setHasServerError(true);
+ experiment.setResult(e.getMessage());
+ }
+ saveExperiment(experiment);
+
+ // Start the process of fetching the status
+ updateWorkflowExperiment(experiment);
+
+ UserActionLogging.LogAction("Run workflow", "Run workflow completed!");
+
+ return new ResponseEntity(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
}
+
+ /**
+ * This method creates a thread that will fetch the workflow result when it is ready
+ *
+ * @param experiment will be used to fetch it's workflow status, it should have the workflowHistoryId initialized
+ * and the result should not already be fetched
+ * @return nothing, just updates the experiment
+ */
+ public void updateWorkflowExperiment(Experiment experiment) {
+
+ if (experiment == null) {
+ UserActionLogging.LogAction("Update workflow experiment", "The experiment does not exist.");
+ return;
+ }
+
+ UserActionLogging.LogAction("Update workflow experiment",
+ " Experiment id : " + experiment.getUuid());
+
+ if (experiment.getWorkflowHistoryId() == null) {
+ UserActionLogging.LogAction("Update workflow experiment", "History Id does not exist.");
+ return;
+ }
+
+ UserActionLogging.LogAction("Update workflow experiment", "Starting Thread..." );
+ new Thread(() -> {
+ while(true) {
+ // ATTENTION: Inside the Thread only LogThreadAction should be used, not LogAction!
+ UserActionLogging.LogThreadAction("Update workflow experiment", "Thread is running...");
+
+ try {
+ sleep(2000);
+ } catch (InterruptedException e) {
+ UserActionLogging.LogThreadAction("Update workflow experiment",
+ "Sleep was disrupted: " + e.getMessage());
+ }
+
+ UserActionLogging.LogThreadAction("Update workflow experiment",
+ "Fetching status for experiment Id: " + experiment.getUuid());
+
+ String state = getWorkflowStatus(experiment.getWorkflowHistoryId());
+ UserActionLogging.LogThreadAction("Update workflow experiment", "State is: " + state);
+
+ switch (state) {
+ case "running":
+ // Do nothing, when the experiment is created the status is set to running
+ UserActionLogging.LogThreadAction("Update workflow experiment",
+ "Workflow is still running.");
+ break;
+
+ case "completed":
+ // Get only the job result that is visible
+ List<GalaxyWorkflowResult> workflowJobsResults = getWorkflowResults(experiment.getWorkflowHistoryId());
+ UserActionLogging.LogThreadAction("Update workflow experiment",
+ "Results are: " + workflowJobsResults.toString());
+
+ boolean resultFound = false;
+ for (GalaxyWorkflowResult jobResult : workflowJobsResults) {
+ if (jobResult.getVisible()) {
+ UserActionLogging.LogThreadAction("Update workflow experiment",
+ "Visible result are: " + jobResult.getId());
+
+ String result = getWorkflowResultBody(experiment.getWorkflowHistoryId(), jobResult.getId());
+
+ UserActionLogging.LogThreadAction("Update workflow experiment", "Result: " + result);
+ if (result == null) {
+ experiment.setHasError(true);
+ experiment.setHasServerError(true);
+ }
+ experiment.setResult("[" + result + "]");
+ experiment.setWorkflowStatus("completed");
+ resultFound = true;
+ }
+ }
+
+ if (!resultFound) { // If there is no visible result
+ UserActionLogging.LogThreadAction("Update workflow experiment", "No visible result");
+ experiment.setResult("[" + new ErrorResponse("The workflow has no visible result.").toString() + "]");
+ experiment.setHasError(true);
+ experiment.setHasServerError(true);
+ }
+
+ finishExperiment(experiment);
+ break;
+
+ case "error":
+ // Get the job result that failed
+ workflowJobsResults = getWorkflowResults(experiment.getWorkflowHistoryId());
+ UserActionLogging.LogThreadAction("Update workflow experiment",
+ "Error results are: " + workflowJobsResults.toString());
+
+ boolean failedJobFound = false;
+ for (GalaxyWorkflowResult jobResult : workflowJobsResults) {
+ if (jobResult.getState().equals("error")) {
+ UserActionLogging.LogThreadAction("Update workflow experiment",
+ "Failed job is: " + jobResult.getId());
+
+ String result = getWorkflowJobError(jobResult.getId());
+
+ UserActionLogging.LogThreadAction("Update workflow experiment", "Job result: " + result);
+ if (result == null) {
+ experiment.setHasError(true);
+ experiment.setHasServerError(true);
+ }
+ experiment.setResult("[" + result + "]");
+ experiment.setWorkflowStatus("error");
+ failedJobFound = true;
+ }
+ }
+
+ if (!failedJobFound) { // If there is no visible failed job
+ UserActionLogging.LogThreadAction("Update workflow experiment", "No failed result");
+ experiment.setResult("[" + new ErrorResponse("The workflow has no failed result.").toString() + "]");
+ experiment.setHasError(true);
+ experiment.setHasServerError(true);
+ }
+ finishExperiment(experiment);
+ break;
+
+ default: // InternalError or unexpected result
+ experiment.setResult("[" + new ErrorResponse("An unexpected error occurred.").toString() + "]");
+ experiment.setHasError(true);
+ experiment.setHasServerError(true);
+ finishExperiment(experiment);
+ break;
+ }
+
+ // If result exists return
+ if (experiment.getResult() != null) {
+ UserActionLogging.LogThreadAction("Update workflow experiment",
+ "Result exists: " + experiment.getResult());
+ return;
+ }
+ }
+ }).start();
+ }
+
+
+ /**
+ * @param historyId The historyId of the workflow
+ * @return "running" -> When the workflow is still running
+ * "internalError" -> When an exception or a bad request occurred
+ * "error" -> When the workflow produced an error
+ * "completed" -> When the workflow completed successfully
+ */
+ public String getWorkflowStatus(String historyId) {
+ // ATTENTION: This function is used from a Thread. Only LogThreadAction should be used, not LogAction!
+ UserActionLogging.LogThreadAction("Get workflow status", " History Id : " + historyId);
+
+ // Create the request client
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ Call<Object> call = service.getWorkflowStatusFromGalaxy(historyId, galaxyApiKey);
+
+ String result = null;
+ try {
+ Response<Object> response = call.execute();
+ if (response.code() >= 400) {
+ UserActionLogging.LogThreadAction("Get workflow status", " Response code: "
+ + response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
+ return "internalError";
+ }
+ result = new Gson().toJson(response.body());
+ UserActionLogging.LogThreadAction("Get workflow status", " Result: " + result);
+
+ } catch (IOException e) {
+ UserActionLogging.LogThreadAction("Get workflow status"
+ , " An exception happened: " + e.getMessage());
+ return "internalError";
+ }
+
+ String state = null;
+ try {
+ JSONObject resultJson = new JSONObject(result);
+ state = resultJson.getString("state");
+ } catch (JSONException e) {
+ UserActionLogging.LogThreadAction("Get workflow status"
+ , " An exception happened: " + e.getMessage());
+ return "internalError";
+ }
+
+ UserActionLogging.LogThreadAction("Get workflow status", " Completed!");
+ switch (state) {
+ case "ok":
+ return "completed";
+ case "error":
+ return "error";
+ case "running":
+ case "new":
+ case "waiting":
+ case "queued":
+ return "running";
+ default:
+ return "internalError";
+ }
+ }
+
+ /**
+ * @param historyId The historyId of the workflow
+ * @return a List<GalaxyWorkflowResult> or null when an error occurred
+ */
+ public List<GalaxyWorkflowResult> getWorkflowResults(String historyId) {
+ UserActionLogging.LogThreadAction("Get workflow results", " historyId : " + historyId);
+
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ Call<List<GalaxyWorkflowResult>> call = service.getWorkflowResultsFromGalaxy(historyId, galaxyApiKey);
+
+ List<GalaxyWorkflowResult> getGalaxyWorkflowResultList = null;
+ try {
+ Response<List<GalaxyWorkflowResult>> response = call.execute();
+ if (response.code() >= 400) {
+ UserActionLogging.LogThreadAction("Get workflow results", " Response code: "
+ + response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
+ return null;
+ }
+ getGalaxyWorkflowResultList = response.body();
+ UserActionLogging.LogThreadAction("Get workflow results", " Result: " + response.body());
+
+ } catch (IOException e) {
+ UserActionLogging.LogThreadAction("Get workflow results"
+ , " An exception happened: " + e.getMessage());
+ return null;
+ }
+
+ UserActionLogging.LogThreadAction("Get workflow results", " Completed!");
+ return getGalaxyWorkflowResultList;
+
+ }
+
+ /**
+ * @param historyId the historyId of the workflow
+ * @param contentId the id of the job result that we want
+ * @return the result of the specific workflow job, null if there was an error
+ */
+ public String getWorkflowResultBody(String historyId, String contentId) {
+ UserActionLogging.LogThreadAction("Get workflow results Body", " historyId : " + historyId);
+
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ Call<Object> call =
+ service.getWorkflowResultsBodyFromGalaxy(historyId, contentId, galaxyApiKey);
+
+ String resultJson = null;
+ try {
+ Response<Object> response = call.execute();
+ if (response.code() >= 400) {
+ UserActionLogging.LogThreadAction("Get workflow results Body", " Response code: "
+ + response.code() + "" + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
+ return null;
+ }
+ resultJson = new Gson().toJson(response.body());
+ UserActionLogging.LogThreadAction("Get workflow results Body", " Result: " + resultJson);
+
+ } catch (IOException e) {
+ UserActionLogging.LogThreadAction("Get workflow results Body",
+ " An exception happened: " + e.getMessage());
+ return null;
+ }
+
+ UserActionLogging.LogThreadAction("Get workflow results Body", " Completed!");
+ return resultJson;
+ }
+
+
+ /**
+ * @param jobId the id of the workflow job that failed
+ * @return the error that was produced or null if an error occurred
+ */
+ public String getWorkflowJobError(String jobId) {
+ UserActionLogging.LogThreadAction("Get workflow job error", " jobId : " + jobId);
+
+ RetroFitGalaxyClients service = RetrofitClientInstance.getRetrofitInstance().create(RetroFitGalaxyClients.class);
+ Call<Object> callError = service.getErrorMessageOfWorkflowFromGalaxy(jobId, galaxyApiKey);
+
+ String fullError = null;
+ String returnError = null;
+ try {
+ Response<Object> response = callError.execute();
+ if (response.code() >= 400) {
+ UserActionLogging.LogThreadAction("Get workflow job error", "Response code: "
+ + response.code() + " with body: " + (response.errorBody() != null ? response.errorBody().string() : " "));
+ return null;
+ }
+
+ // Parsing the stderr of the job that failed
+ String jsonString = new Gson().toJson(response.body());
+ JsonElement jsonElement = new JsonParser().parse(jsonString);
+ JsonObject rootObject = jsonElement.getAsJsonObject();
+ fullError = rootObject.get("stderr").getAsString();
+ UserActionLogging.LogThreadAction("Get workflow job error", "Error: " + fullError);
+
+ String[] arrOfStr = fullError.split("ValueError", 0);
+ String specError = arrOfStr[arrOfStr.length - 1];
+ returnError = specError.substring(1);
+ UserActionLogging.LogThreadAction("Get workflow job error", "Parsed Error: " + returnError);
+
+ } catch (IOException e) {
+ UserActionLogging.LogThreadAction("Get workflow job error", "Exception: " + e.getMessage());
+ return null;
+ }
+
+ UserActionLogging.LogThreadAction("Get workflow job error", "Completed successfully!");
+
+ return returnError;
+ }
+
+
}
diff --git a/src/main/java/eu/hbp/mip/controllers/JWTApi.java b/src/main/java/eu/hbp/mip/controllers/JWTApi.java
deleted file mode 100644
index a1cb6afd55431bb859170b52c9daa7007ca69c42..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/controllers/JWTApi.java
+++ /dev/null
@@ -1,40 +0,0 @@
-package eu.hbp.mip.controllers;
-
-import static org.springframework.http.MediaType.TEXT_PLAIN_VALUE;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.http.ResponseEntity;
-import org.springframework.http.HttpStatus;
-import eu.hbp.mip.model.User;
-import eu.hbp.mip.model.UserInfo;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.web.bind.annotation.*;
-import io.swagger.annotations.Api;
-import io.swagger.annotations.ApiOperation;
-import eu.hbp.mip.utils.JWTUtil;
-import eu.hbp.mip.utils.UserActionLogging;
-
-@RestController
-@RequestMapping(value = "/jwt", produces = { TEXT_PLAIN_VALUE })
-@Api(value = "/jwt", description = "the jwt API")
-public class JWTApi {
-
- @Autowired
- private UserInfo userInfo;
-
- @Value("#{'${services.workflows.jwtSecret}'}")
- private String jwtSecret;
-
- @ApiOperation(value = "Create a JSON Web Token", response = String.class)
- @RequestMapping(method = RequestMethod.POST)
- public ResponseEntity<String> createJWT() {
-
- UserActionLogging.LogAction("Create a JSON Web Token", "");
-
- User user = userInfo.getUser();
- String token = JWTUtil.getJWT(jwtSecret, user.getEmail());
-
- return ResponseEntity.status(HttpStatus.CREATED).body(token);
- }
-}
diff --git a/src/main/java/eu/hbp/mip/controllers/MethodsApi.java b/src/main/java/eu/hbp/mip/controllers/MethodsApi.java
deleted file mode 100644
index f88f6795156f566b4b4e6e70288a5e4d535a67da..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/controllers/MethodsApi.java
+++ /dev/null
@@ -1,77 +0,0 @@
-package eu.hbp.mip.controllers;
-
-import com.google.gson.*;
-import io.swagger.annotations.Api;
-import io.swagger.annotations.ApiOperation;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.http.ResponseEntity;
-import org.springframework.web.bind.annotation.*;
-import eu.hbp.mip.model.User;
-import eu.hbp.mip.model.UserInfo;
-import eu.hbp.mip.utils.HTTPUtil;
-import org.springframework.beans.factory.annotation.Value;
-import java.io.IOException;
-import eu.hbp.mip.utils.JWTUtil;
-import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
-import org.springframework.beans.factory.annotation.Autowired;
-import eu.hbp.mip.utils.UserActionLogging;
-
-@RestController
-@RequestMapping(value = "/methods", produces = { APPLICATION_JSON_VALUE })
-@Api(value = "/methods", description = "the methods API")
-public class MethodsApi {
-
-
- private static final Gson gson = new Gson();
-
- @Value("#{'${services.exareme.algorithmsUrl:http://localhost:9090/mining/algorithms.json}'}")
- private String exaremeAlgorithmsUrl;
-
- @Value("#{'${services.workflows.workflowUrl}'}")
- private String workflowUrl;
-
- @Value("#{'${services.workflows.jwtSecret}'}")
- private String jwtSecret;
-
- @Autowired
- private UserInfo userInfo;
-
- @ApiOperation(value = "List Exareme algorithms and validations", response = String.class)
- @RequestMapping(value = "/exareme", method = RequestMethod.GET)
- public ResponseEntity<Object> getExaremeAlgorithms() {
- UserActionLogging.LogAction("List Exareme algorithms and validations", "");
-
- try {
- StringBuilder response = new StringBuilder();
- HTTPUtil.sendGet(exaremeAlgorithmsUrl, response);
- JsonElement element = new JsonParser().parse(response.toString());
-
- return ResponseEntity.ok(gson.toJson(element));
- } catch (IOException e) {
- return ResponseEntity.status(500).body(e.getMessage());
- }
-
- }
-
- @ApiOperation(value = "List Galaxy workflows", response = String.class)
- @RequestMapping(value = "/workflows", method = RequestMethod.GET)
- public ResponseEntity<Object> getWorkflows() {
- UserActionLogging.LogAction("List Galaxy workflows", "");
-
- try {
- User user = userInfo.getUser();
- String token = JWTUtil.getJWT(jwtSecret, user.getEmail());
-
- StringBuilder response = new StringBuilder();
- HTTPUtil.sendAuthorizedHTTP(workflowUrl + "/getAllWorkflowWithDetails", "", response, "GET", "Bearer " + token);
- JsonElement element = new JsonParser().parse(response.toString());
-
- return ResponseEntity.ok(gson.toJson(element));
- } catch (IOException e) {
- return ResponseEntity.status(500).body(e.getMessage());
- }
-
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/controllers/MiningApi.java b/src/main/java/eu/hbp/mip/controllers/MiningApi.java
index 13272fc7355ed509e5b030429409a98b83ac55e1..3adcc6269e8120147c6c81367c91b928c1d5d486 100644
--- a/src/main/java/eu/hbp/mip/controllers/MiningApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/MiningApi.java
@@ -45,16 +45,16 @@ public class MiningApi {
@Autowired
private UserInfo userInfo;
- @Value("#{'${services.exareme.miningExaremeUrl:http://localhost:9090/mining/query}'}")
- public String miningExaremeQueryUrl;
+ @Value("#{'${services.exareme.queryExaremeUrl:http://localhost:9090/mining/query}'}")
+ public String queryExaremeUrl;
- @ApiOperation(value = "Create an histogram on Exareme", response = String.class)
- @RequestMapping(value = "/exareme", method = RequestMethod.POST)
- public ResponseEntity runExaremeMining(@RequestBody List<HashMap<String, String>> queryList) {
+ @ApiOperation(value = "Create a histogram on Exareme", response = String.class)
+ @RequestMapping(value = "/histograms", method = RequestMethod.POST)
+ public ResponseEntity runExaremeHistograms(@RequestBody List<HashMap<String, String>> queryList) {
UserActionLogging.LogAction("Run an histogram", "");
String query = gson.toJson(queryList);
- String url = miningExaremeQueryUrl + "/" + "HISTOGRAMS";
+ String url = queryExaremeUrl + "/" + "MULTIPLE_HISTOGRAMS";
try {
StringBuilder results = new StringBuilder();
@@ -66,13 +66,13 @@ public class MiningApi {
}
}
- @ApiOperation(value = "Create an descriptive statistic on Exareme", response = String.class)
- @RequestMapping(value = "/exareme-stats", method = RequestMethod.POST)
+ @ApiOperation(value = "Create a descriptive statistic on Exareme", response = String.class)
+ @RequestMapping(value = "/descriptive_stats", method = RequestMethod.POST)
public ResponseEntity runExaremeDescriptiveStats(@RequestBody List<HashMap<String, String>> queryList) {
UserActionLogging.LogAction("Run descriptive stats", "");
String query = gson.toJson(queryList);
- String url = miningExaremeQueryUrl + "/" + "DESCRIPTIVE_STATS";
+ String url = queryExaremeUrl + "/" + "DESCRIPTIVE_STATS";
try {
StringBuilder results = new StringBuilder();
@@ -84,24 +84,11 @@ public class MiningApi {
}
}
- @ApiOperation(value = "Perform an non persisted algorithm on Exareme", response = String.class)
- @RequestMapping(value = "/exareme/{algorithmName}", method = RequestMethod.POST)
- public ResponseEntity runExaremeAlgorithm(
- @RequestBody List<HashMap<String, String>> queryList,
- @ApiParam(value = "algorithmName", required = true) @PathVariable("algorithmName") String algorithmName
- ) {
- UserActionLogging.LogAction("Run algo", "");
+ @ApiOperation(value = "Check if a formula is valid", response = String.class)
+ @RequestMapping(value = "/checkFormula", method = RequestMethod.POST)
+ public ResponseEntity checkFormulaValidity(String formula) {
+ UserActionLogging.LogAction("Check Formula Validity", "");
- String query = gson.toJson(queryList);
- String url = miningExaremeQueryUrl + "/" + algorithmName;
-
- try {
- StringBuilder results = new StringBuilder();
- int code = HTTPUtil.sendPost(url, query, results);
-
- return ResponseEntity.ok(gson.toJson(results.toString()));
- } catch (IOException e) {
- return new ResponseEntity<>("Not found", HttpStatus.BAD_REQUEST);
- }
+ return ResponseEntity.ok("");
}
}
diff --git a/src/main/java/eu/hbp/mip/controllers/galaxy/retrofit/RetroFitGalaxyClients.java b/src/main/java/eu/hbp/mip/controllers/galaxy/retrofit/RetroFitGalaxyClients.java
new file mode 100644
index 0000000000000000000000000000000000000000..612dce6ca5b557f23deafdf873978c0f442eb1d9
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/controllers/galaxy/retrofit/RetroFitGalaxyClients.java
@@ -0,0 +1,31 @@
+package eu.hbp.mip.controllers.galaxy.retrofit;
+
+import com.google.gson.JsonObject;
+import eu.hbp.mip.model.galaxy.GalaxyWorkflowResult;
+import eu.hbp.mip.model.galaxy.PostWorkflowToGalaxyDtoResponse;
+import eu.hbp.mip.model.galaxy.WorkflowDTO;
+import retrofit2.Call;
+import retrofit2.http.*;
+
+import java.util.List;
+
+public interface RetroFitGalaxyClients {
+
+ @GET("workflows/{workflowId}")
+ Call<WorkflowDTO> getWorkflowFromGalaxy(@Path("workflowId") String workflowId, @Query("key") String key);
+
+ @POST("workflows/{workflowId}/invocations")
+ Call<PostWorkflowToGalaxyDtoResponse> postWorkflowToGalaxy(@Path("workflowId") String workflowId, @Query("key") String key, @Body JsonObject body);
+
+ @GET("histories/{historyId}")
+ Call<Object> getWorkflowStatusFromGalaxy(@Path("historyId") String historyId, @Query("key") String key);
+
+ @GET("histories/{historyId}/contents")
+ Call<List<GalaxyWorkflowResult>> getWorkflowResultsFromGalaxy(@Path("historyId") String historyId, @Query("key") String key);
+
+ @GET("histories/{historyId}/contents/{contentId}/display")
+ Call<Object> getWorkflowResultsBodyFromGalaxy(@Path("historyId") String historyId, @Path("contentId") String contentId, @Query("key") String key);
+
+ @GET("jobs/{jobId}?full=true")
+ Call<Object> getErrorMessageOfWorkflowFromGalaxy(@Path("jobId") String jobId, @Query("key") String key);
+}
\ No newline at end of file
diff --git a/src/main/java/eu/hbp/mip/controllers/galaxy/retrofit/RetrofitClientInstance.java b/src/main/java/eu/hbp/mip/controllers/galaxy/retrofit/RetrofitClientInstance.java
new file mode 100644
index 0000000000000000000000000000000000000000..6aa218902ebd724518d56d8cca8b0c5e77aa2893
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/controllers/galaxy/retrofit/RetrofitClientInstance.java
@@ -0,0 +1,42 @@
+package eu.hbp.mip.controllers.galaxy.retrofit;
+
+import okhttp3.OkHttpClient;
+import okhttp3.logging.HttpLoggingInterceptor;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.stereotype.Component;
+import retrofit2.Retrofit;
+import retrofit2.converter.gson.GsonConverterFactory;
+
+import javax.annotation.PostConstruct;
+
+@Component
+public class RetrofitClientInstance {
+
+ private static Retrofit retrofit;
+
+ @Value("#{'${services.galaxy.galaxyUrl}'}")
+ private String galaxyUrl;
+
+ private static String BASE_URL;
+
+ @PostConstruct
+ public void init() {
+ BASE_URL = galaxyUrl + "/api/";
+ }
+
+ public static Retrofit getRetrofitInstance() {
+ if (retrofit == null) {
+
+ HttpLoggingInterceptor interceptor = new HttpLoggingInterceptor();
+ interceptor.setLevel(HttpLoggingInterceptor.Level.BODY);
+ OkHttpClient client = new OkHttpClient.Builder().addInterceptor(interceptor).build();
+
+ retrofit = new retrofit2.Retrofit.Builder()
+ .baseUrl(BASE_URL)
+ .client(client)
+ .addConverterFactory(GsonConverterFactory.create())
+ .build();
+ }
+ return retrofit;
+ }
+}
\ No newline at end of file
diff --git a/src/main/java/eu/hbp/mip/model/Algorithm.java b/src/main/java/eu/hbp/mip/model/Algorithm.java
deleted file mode 100644
index bd08093a82e0cc7823fdc6c33c193a3feff774ba..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/Algorithm.java
+++ /dev/null
@@ -1,32 +0,0 @@
-package eu.hbp.mip.model;
-
-import java.util.LinkedList;
-
-/**
- * Created by mirco on 09.11.16.
- */
-
-public class Algorithm extends ExperimentValidator {
-
- private boolean validation;
-
- public Algorithm() {
-
- }
-
- public Algorithm(String code, String name, boolean validation) {
- this.validation = validation;
- setCode(code);
- setName(name);
- setParameters(new LinkedList<>());
- }
-
- public boolean isValidation() {
- return validation;
- }
-
- public void setValidation(boolean validation) {
- this.validation = validation;
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/AlgorithmDTO.java b/src/main/java/eu/hbp/mip/model/AlgorithmDTO.java
new file mode 100644
index 0000000000000000000000000000000000000000..ed0ef2a15606ef09f139bad65c90c3cf436c2474
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/model/AlgorithmDTO.java
@@ -0,0 +1,220 @@
+package eu.hbp.mip.model;
+
+import com.google.gson.annotations.SerializedName;
+
+import java.util.List;
+
+public class AlgorithmDTO {
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public String getDesc() {
+ return desc;
+ }
+
+ public void setDesc(String desc) {
+ this.desc = desc;
+ }
+
+ public String getLabel() {
+ return label;
+ }
+
+ public void setLabel(String label) {
+ this.label = label;
+ }
+
+ public String getType() {
+ return type;
+ }
+
+ public void setType(String type) {
+ this.type = type;
+ }
+
+ public List<AlgorithmParamDTO> getParameters() {
+ return parameters;
+ }
+
+ public void setParameters(List<AlgorithmParamDTO> parameters) {
+ this.parameters = parameters;
+ }
+
+ @SerializedName("name")
+ private String name;
+
+ @SerializedName("desc")
+ private String desc;
+
+ @SerializedName("label")
+ private String label;
+
+ @SerializedName("type")
+ private String type;
+
+ @SerializedName("parameters")
+ private List<AlgorithmParamDTO> parameters;
+
+ public static class AlgorithmParamDTO {
+ @SerializedName("name")
+ private String name;
+
+ @SerializedName("desc")
+ private String desc;
+
+ @SerializedName("label")
+ private String label;
+
+ @SerializedName("type")
+ private String type;
+
+ @SerializedName("columnValuesSQLType")
+ private String columnValuesSQLType;
+
+ @SerializedName("columnValuesIsCategorical")
+ private String columnValuesIsCategorical;
+
+ @SerializedName("value")
+ private String value;
+
+ @SerializedName("defaultValue")
+ private String defaultValue;
+
+ @SerializedName("valueType")
+ private String valueType;
+
+ @SerializedName("valueNotBlank")
+ private String valueNotBlank;
+
+ @SerializedName("valueMultiple")
+ private String valueMultiple;
+
+ @SerializedName("valueMin")
+ private String valueMin;
+
+ @SerializedName("valueMax")
+ private String valueMax;
+
+ @SerializedName("valueEnumerations")
+ private List<String> valueEnumerations;
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public String getDesc() {
+ return desc;
+ }
+
+ public void setDesc(String desc) {
+ this.desc = desc;
+ }
+
+ public String getLabel() {
+ return label;
+ }
+
+ public void setLabel(String label) {
+ this.label = label;
+ }
+
+ public String getType() {
+ return type;
+ }
+
+ public void setType(String type) {
+ this.type = type;
+ }
+
+ public String getColumnValuesSQLType() {
+ return columnValuesSQLType;
+ }
+
+ public void setColumnValuesSQLType(String columnValuesSQLType) {
+ this.columnValuesSQLType = columnValuesSQLType;
+ }
+
+ public String getColumnValuesIsCategorical() {
+ return columnValuesIsCategorical;
+ }
+
+ public void setColumnValuesIsCategorical(String columnValuesIsCategorical) {
+ this.columnValuesIsCategorical = columnValuesIsCategorical;
+ }
+
+ public String getValue() {
+ return value;
+ }
+
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ public String getDefaultValue() {
+ return defaultValue;
+ }
+
+ public void setDefaultValue(String defaultValue) {
+ this.defaultValue = defaultValue;
+ }
+
+ public String getValueType() {
+ return valueType;
+ }
+
+ public void setValueType(String valueType) {
+ this.valueType = valueType;
+ }
+
+ public String getValueNotBlank() {
+ return valueNotBlank;
+ }
+
+ public void setValueNotBlank(String valueNotBlank) {
+ this.valueNotBlank = valueNotBlank;
+ }
+
+ public String getValueMultiple() {
+ return valueMultiple;
+ }
+
+ public void setValueMultiple(String valueMultiple) {
+ this.valueMultiple = valueMultiple;
+ }
+
+ public String getValueMin() {
+ return valueMin;
+ }
+
+ public void setValueMin(String valueMin) {
+ this.valueMin = valueMin;
+ }
+
+ public String getValueMax() {
+ return valueMax;
+ }
+
+ public void setValueMax(String valueMax) {
+ this.valueMax = valueMax;
+ }
+
+ public List<String> getValueEnumerations() {
+ return valueEnumerations;
+ }
+
+ public void setValueEnumerations(List<String> valueEnumerations) {
+ this.valueEnumerations = valueEnumerations;
+ }
+ }
+
+}
diff --git a/src/main/java/eu/hbp/mip/model/AlgorithmParam.java b/src/main/java/eu/hbp/mip/model/AlgorithmParam.java
deleted file mode 100644
index 62c48ba13b4cffcf647d4da97a0509735f18cac4..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/AlgorithmParam.java
+++ /dev/null
@@ -1,36 +0,0 @@
-package eu.hbp.mip.model;
-
-/**
- * Created by mirco on 09.11.16.
- */
-
-public class AlgorithmParam {
-
- private String code;
- private String value;
-
- public String getCode() {
- return code;
-
- }
-
- public void setName(String name) {
- this.code = name;
- }
-
- public String getName() {
- return this.code;
- }
-
- public void setCode(String code) {
- this.code = code;
- }
-
- public String getValue() {
- return value;
- }
-
- public void setValue(String value) {
- this.value = value;
- }
-}
diff --git a/src/main/java/eu/hbp/mip/model/Experiment.java b/src/main/java/eu/hbp/mip/model/Experiment.java
index a15b575c9b76895d922d7c65b3c0ea3811501a7e..902cf37da1ef0abad1f2c8836fe0a7e2654f077f 100644
--- a/src/main/java/eu/hbp/mip/model/Experiment.java
+++ b/src/main/java/eu/hbp/mip/model/Experiment.java
@@ -16,8 +16,6 @@ import java.util.*;
@Table(name = "`experiment`")
public class Experiment {
- private static final Logger LOGGER = LoggerFactory.getLogger(Experiment.class);
-
private static final Gson gson = new Gson();
@Id
@@ -45,9 +43,16 @@ public class Experiment {
private String algorithms;
@Column(columnDefinition="TEXT")
- @Expose
private String validations;
+ @Column(columnDefinition="TEXT")
+ @Expose
+ private String workflowHistoryId;
+
+ @Column(columnDefinition="TEXT")
+ @Expose
+ private String workflowStatus;
+
@Column(columnDefinition="TEXT")
@Expose
private String result;
@@ -139,6 +144,22 @@ public class Experiment {
this.hasError = hasError;
}
+ public String getWorkflowHistoryId() {
+ return workflowHistoryId;
+ }
+
+ public void setWorkflowHistoryId(String workflowHistoryId) {
+ this.workflowHistoryId = workflowHistoryId;
+ }
+
+ public String getWorkflowStatus() {
+ return workflowStatus;
+ }
+
+ public void setWorkflowStatus(String workflowStatus) {
+ this.workflowStatus = workflowStatus;
+ }
+
public String getResult() {
return result;
}
diff --git a/src/main/java/eu/hbp/mip/model/ExperimentExecutionDTO.java b/src/main/java/eu/hbp/mip/model/ExperimentExecutionDTO.java
new file mode 100644
index 0000000000000000000000000000000000000000..a68cd9121d852503bc01eb6b2f0d23dd8af525dd
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/model/ExperimentExecutionDTO.java
@@ -0,0 +1,106 @@
+package eu.hbp.mip.model;
+
+import java.util.List;
+
+public class ExperimentExecutionDTO {
+
+ private String name;
+ private String model;
+ private List<AlgorithmExecutionDTO> algorithms;
+
+ public String getModel() {
+ return model;
+ }
+
+ public void setModel(String model) {
+ this.model = model;
+ }
+
+ public List<AlgorithmExecutionDTO> getAlgorithms() {
+ return algorithms;
+ }
+
+ public void setAlgorithms(List<AlgorithmExecutionDTO> algorithms) {
+ this.algorithms = algorithms;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public static class AlgorithmExecutionDTO {
+
+ private String name;
+ private String label;
+ private String type;
+
+ private List<AlgorithmExecutionParamDTO> parameters;
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public String getType() {
+ return type;
+ }
+
+ public void setType(String type) {
+ this.type = type;
+ }
+
+ public List<AlgorithmExecutionDTO.AlgorithmExecutionParamDTO> getParameters() {
+ return parameters;
+ }
+
+ public void setParameters(List<AlgorithmExecutionDTO.AlgorithmExecutionParamDTO> parameters) {
+ this.parameters = parameters;
+ }
+
+ public String getLabel() {
+ return label;
+ }
+
+ public void setLabel(String label) {
+ this.label = label;
+ }
+
+ public static class AlgorithmExecutionParamDTO {
+
+ private String name;
+ private String label;
+ private String value;
+
+ public String getName() {
+ return this.name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public String getValue() {
+ return value;
+ }
+
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ public String getLabel() {
+ return label;
+ }
+
+ public void setLabel(String label) {
+ this.label = label;
+ }
+ }
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/model/ExperimentQuery.java b/src/main/java/eu/hbp/mip/model/ExperimentQuery.java
deleted file mode 100644
index 333751c438099de62942918e17f019505a800de7..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/ExperimentQuery.java
+++ /dev/null
@@ -1,46 +0,0 @@
-package eu.hbp.mip.model;
-
-import java.util.List;
-
-/**
- * Created by mirco on 09.11.16.
- */
-public class ExperimentQuery {
-
- private String name;
- private String model;
- private List<ExperimentValidator> validations;
- private List<Algorithm> algorithms;
-
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public String getModel() {
- return model;
- }
-
- public void setModel(String model) {
- this.model = model;
- }
-
- public List<ExperimentValidator> getValidations() {
- return validations;
- }
-
- public void setValidations(List<ExperimentValidator> validations) {
- this.validations = validations;
- }
-
- public List<Algorithm> getAlgorithms() {
- return algorithms;
- }
-
- public void setAlgorithms(List<Algorithm> algorithms) {
- this.algorithms = algorithms;
- }
-}
diff --git a/src/main/java/eu/hbp/mip/model/ExperimentValidator.java b/src/main/java/eu/hbp/mip/model/ExperimentValidator.java
deleted file mode 100644
index 208fc90fa7272779bf51e09ca7fa0b6f409c66d3..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/model/ExperimentValidator.java
+++ /dev/null
@@ -1,40 +0,0 @@
-package eu.hbp.mip.model;
-
-import java.util.List;
-
-/**
- * Created by mirco on 09.11.16.
- */
-
-public class ExperimentValidator {
-
- private String code;
- private String name;
-
- private List<AlgorithmParam> parameters;
-
- public String getCode() {
- return code;
- }
-
- public void setCode(String code) {
- this.code = code;
- }
-
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public List<AlgorithmParam> getParameters() {
- return parameters;
- }
-
- public void setParameters(List<AlgorithmParam> parameters) {
- this.parameters = parameters;
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/model/MiningQuery.java b/src/main/java/eu/hbp/mip/model/MiningQuery.java
index 6ced265037ba4148d4f18e6ba06d9434e4610317..171c55032eee4b3c5f63d636c137d6ae41bfe051 100644
--- a/src/main/java/eu/hbp/mip/model/MiningQuery.java
+++ b/src/main/java/eu/hbp/mip/model/MiningQuery.java
@@ -1,6 +1,7 @@
package eu.hbp.mip.model;
import com.google.gson.Gson;
+
import java.util.LinkedList;
import java.util.List;
@@ -14,7 +15,7 @@ public class MiningQuery {
private List<Variable> grouping;
private List<Variable> datasets;
private String filters;
- private Algorithm algorithm;
+ private ExperimentExecutionDTO.AlgorithmExecutionDTO algorithm;
public MiningQuery() {
this.variables = new LinkedList<>();
@@ -32,7 +33,9 @@ public class MiningQuery {
this.variables = variables;
}
- public void addVariable(Variable variable) { this.variables.add(variable); }
+ public void addVariable(Variable variable) {
+ this.variables.add(variable);
+ }
public List<Variable> getCovariables() {
return covariables;
@@ -42,7 +45,9 @@ public class MiningQuery {
this.covariables = covariables;
}
- public void addCovariable(Variable variable) { this.covariables.add(variable); }
+ public void addCovariable(Variable variable) {
+ this.covariables.add(variable);
+ }
public List<Variable> getGrouping() {
return grouping;
@@ -52,15 +57,21 @@ public class MiningQuery {
this.grouping = grouping;
}
- public List<Variable> getDatasets() { return datasets; }
+ public List<Variable> getDatasets() {
+ return datasets;
+ }
public void setDataset(List<Variable> datasets) {
this.datasets = datasets;
}
- public void addDataset(Variable variable) { this.datasets.add(variable); }
+ public void addDataset(Variable variable) {
+ this.datasets.add(variable);
+ }
- public void addGrouping(Variable variable) { this.grouping.add(variable); }
+ public void addGrouping(Variable variable) {
+ this.grouping.add(variable);
+ }
public String getFilters() {
return filters;
@@ -70,11 +81,11 @@ public class MiningQuery {
this.filters = filters;
}
- public Algorithm getAlgorithm() {
+ public ExperimentExecutionDTO.AlgorithmExecutionDTO getAlgorithm() {
return algorithm;
}
- public void setAlgorithm(Algorithm algorithm) {
+ public void setAlgorithm(ExperimentExecutionDTO.AlgorithmExecutionDTO algorithm) {
this.algorithm = algorithm;
}
diff --git a/src/main/java/eu/hbp/mip/model/galaxy/ErrorResponse.java b/src/main/java/eu/hbp/mip/model/galaxy/ErrorResponse.java
new file mode 100644
index 0000000000000000000000000000000000000000..77a171358b54561e3492dcb317acd835aeaa645f
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/model/galaxy/ErrorResponse.java
@@ -0,0 +1,50 @@
+/*
+ * Developed by Kechagias Konstantinos.
+ * Copyright (c) 2019. MIT License
+ */
+
+package eu.hbp.mip.model.galaxy;
+
+import com.google.gson.annotations.SerializedName;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class ErrorResponse {
+
+ @SerializedName("result")
+ List<ErrorMessage> result;
+
+ public ErrorResponse() {
+ }
+
+ public ErrorResponse(String errMsg) {
+ this.result = new ArrayList<>();
+ this.result.add(new ErrorMessage(errMsg));
+ }
+
+ public static class ErrorMessage {
+
+ @SerializedName("data")
+ String errMsg;
+
+ @SerializedName("type")
+ String errType;
+
+ public ErrorMessage() {
+ }
+
+ public ErrorMessage(String errMsg) {
+ this.errMsg = errMsg;
+ this.errType = "text/plain+error";
+ }
+
+ public String getErrMsg() {
+ return errMsg;
+ }
+
+ public void setErrMsg(String errMsg) {
+ this.errMsg = errMsg;
+ }
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/model/galaxy/GalaxyWorkflowResult.java b/src/main/java/eu/hbp/mip/model/galaxy/GalaxyWorkflowResult.java
new file mode 100644
index 0000000000000000000000000000000000000000..089a6a626ed1e0d38306c911b515edd3fa8fa5f0
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/model/galaxy/GalaxyWorkflowResult.java
@@ -0,0 +1,208 @@
+/*
+ * Developed by Kechagias Konstantinos.
+ * Copyright (c) 2019. MIT License
+ */
+
+package eu.hbp.mip.model.galaxy;
+
+import com.google.gson.annotations.SerializedName;
+
+import java.util.List;
+
+public class GalaxyWorkflowResult {
+
+ @SerializedName("history_content_type")
+ private String historyContentType;
+ @SerializedName("update_time")
+ private String updateTime;
+ @SerializedName("name")
+ private String name;
+ @SerializedName("extension")
+ private String extension;
+ @SerializedName("type_id")
+ private String typeId;
+ @SerializedName("deleted")
+ private Boolean deleted;
+ @SerializedName("history_id")
+ private String historyId;
+ @SerializedName("tags")
+ private List<Object> tags = null;
+ @SerializedName("id")
+ private String id;
+ @SerializedName("visible")
+ private Boolean visible;
+ @SerializedName("state")
+ private String state;
+ @SerializedName("create_time")
+ private String createTime;
+ @SerializedName("hid")
+ private Integer hid;
+ @SerializedName("url")
+ private String url;
+ @SerializedName("dataset_id")
+ private String datasetId;
+ @SerializedName("type")
+ private String type;
+ @SerializedName("purged")
+ private Boolean purged;
+
+ public GalaxyWorkflowResult() {
+ }
+
+ public GalaxyWorkflowResult(String historyContentType, String updateTime, String name, String extension, String typeId, Boolean deleted, String historyId, List<Object> tags, String id, Boolean visible, String state, String createTime, Integer hid, String url, String datasetId, String type, Boolean purged) {
+ this.historyContentType = historyContentType;
+ this.updateTime = updateTime;
+ this.name = name;
+ this.extension = extension;
+ this.typeId = typeId;
+ this.deleted = deleted;
+ this.historyId = historyId;
+ this.tags = tags;
+ this.id = id;
+ this.visible = visible;
+ this.state = state;
+ this.createTime = createTime;
+ this.hid = hid;
+ this.url = url;
+ this.datasetId = datasetId;
+ this.type = type;
+ this.purged = purged;
+ }
+
+ public String getHistoryContentType() {
+ return historyContentType;
+ }
+
+ public void setHistoryContentType(String historyContentType) {
+ this.historyContentType = historyContentType;
+ }
+
+ public String getUpdateTime() {
+ return updateTime;
+ }
+
+ public void setUpdateTime(String updateTime) {
+ this.updateTime = updateTime;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public String getExtension() {
+ return extension;
+ }
+
+ public void setExtension(String extension) {
+ this.extension = extension;
+ }
+
+ public String getTypeId() {
+ return typeId;
+ }
+
+ public void setTypeId(String typeId) {
+ this.typeId = typeId;
+ }
+
+ public Boolean getDeleted() {
+ return deleted;
+ }
+
+ public void setDeleted(Boolean deleted) {
+ this.deleted = deleted;
+ }
+
+ public String getHistoryId() {
+ return historyId;
+ }
+
+ public void setHistoryId(String historyId) {
+ this.historyId = historyId;
+ }
+
+ public List<Object> getTags() {
+ return tags;
+ }
+
+ public void setTags(List<Object> tags) {
+ this.tags = tags;
+ }
+
+ public String getId() {
+ return id;
+ }
+
+ public void setId(String id) {
+ this.id = id;
+ }
+
+ public Boolean getVisible() {
+ return visible;
+ }
+
+ public void setVisible(Boolean visible) {
+ this.visible = visible;
+ }
+
+ public String getState() {
+ return state;
+ }
+
+ public void setState(String state) {
+ this.state = state;
+ }
+
+ public String getCreateTime() {
+ return createTime;
+ }
+
+ public void setCreateTime(String createTime) {
+ this.createTime = createTime;
+ }
+
+ public Integer getHid() {
+ return hid;
+ }
+
+ public void setHid(Integer hid) {
+ this.hid = hid;
+ }
+
+ public String getUrl() {
+ return url;
+ }
+
+ public void setUrl(String url) {
+ this.url = url;
+ }
+
+ public String getDatasetId() {
+ return datasetId;
+ }
+
+ public void setDatasetId(String datasetId) {
+ this.datasetId = datasetId;
+ }
+
+ public String getType() {
+ return type;
+ }
+
+ public void setType(String type) {
+ this.type = type;
+ }
+
+ public Boolean getPurged() {
+ return purged;
+ }
+
+ public void setPurged(Boolean purged) {
+ this.purged = purged;
+ }
+}
+
diff --git a/src/main/java/eu/hbp/mip/model/galaxy/PostWorkflowToGalaxyDtoResponse.java b/src/main/java/eu/hbp/mip/model/galaxy/PostWorkflowToGalaxyDtoResponse.java
new file mode 100644
index 0000000000000000000000000000000000000000..edefd63266a8d1678bf82d057882e4eccab112cc
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/model/galaxy/PostWorkflowToGalaxyDtoResponse.java
@@ -0,0 +1,93 @@
+/*
+ * Developed by Kechagias Konstantinos.
+ * Copyright (c) 2019. MIT License
+ */
+
+package eu.hbp.mip.model.galaxy;
+
+import com.google.gson.annotations.SerializedName;
+
+public class PostWorkflowToGalaxyDtoResponse {
+
+
+ @SerializedName("update_time")
+ String updateTime;
+ String uuid;
+ @SerializedName("history_id")
+ String historyId;
+ String stake;
+ @SerializedName("workflow_id")
+ String workflowId;
+ @SerializedName("model_class")
+ String modelClass;
+ String id;
+
+ public PostWorkflowToGalaxyDtoResponse() {
+ }
+
+ public PostWorkflowToGalaxyDtoResponse(String updateTime, String uuid, String historyId, String stake, String workflowId, String modelClass, String id) {
+ this.updateTime = updateTime;
+ this.uuid = uuid;
+ this.historyId = historyId;
+ this.stake = stake;
+ this.workflowId = workflowId;
+ this.modelClass = modelClass;
+ this.id = id;
+ }
+
+ public String getUpdateTime() {
+ return updateTime;
+ }
+
+ public void setUpdateTime(String updateTime) {
+ this.updateTime = updateTime;
+ }
+
+ public String getUuid() {
+ return uuid;
+ }
+
+ public void setUuid(String uuid) {
+ this.uuid = uuid;
+ }
+
+ public String getHistoryId() {
+ return historyId;
+ }
+
+ public void setHistoryId(String historyId) {
+ this.historyId = historyId;
+ }
+
+ public String getStake() {
+ return stake;
+ }
+
+ public void setStake(String stake) {
+ this.stake = stake;
+ }
+
+ public String getWorkflowId() {
+ return workflowId;
+ }
+
+ public void setWorkflowId(String workflowId) {
+ this.workflowId = workflowId;
+ }
+
+ public String getModelClass() {
+ return modelClass;
+ }
+
+ public void setModelClass(String modelClass) {
+ this.modelClass = modelClass;
+ }
+
+ public String getId() {
+ return id;
+ }
+
+ public void setId(String id) {
+ this.id = id;
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/model/galaxy/WorkflowDTO.java b/src/main/java/eu/hbp/mip/model/galaxy/WorkflowDTO.java
new file mode 100644
index 0000000000000000000000000000000000000000..de537a1dcc4649e0ea6b28ff967567b599c77251
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/model/galaxy/WorkflowDTO.java
@@ -0,0 +1,162 @@
+package eu.hbp.mip.model.galaxy;
+
+import com.google.gson.Gson;
+import com.google.gson.annotations.SerializedName;
+import eu.hbp.mip.model.AlgorithmDTO;
+
+import java.util.*;
+
+public class WorkflowDTO {
+
+ @SerializedName("id")
+ private String id;
+
+ @SerializedName("name")
+ private String name;
+
+ @SerializedName("inputs")
+ private HashMap<String, WorkflowInputDTO> inputs;
+
+ @SerializedName("steps")
+ private HashMap<String, WorkflowStepDTO> steps;
+
+ public String getId() {
+ return id;
+ }
+
+ public void setId(String id) {
+ this.id = id;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public HashMap<String, WorkflowInputDTO> getInputs() {
+ return inputs;
+ }
+
+ public void setInputs(HashMap<String, WorkflowInputDTO> inputs) {
+ this.inputs = inputs;
+ }
+
+ public HashMap<String, WorkflowStepDTO> getSteps() {
+ return steps;
+ }
+
+ public void setSteps(HashMap<String, WorkflowStepDTO> steps) {
+ this.steps = steps;
+ }
+
+ public class WorkflowInputDTO {
+ @SerializedName("uuid")
+ private String uuid;
+
+ @SerializedName("label")
+ private String label;
+
+ public String getLabel() {
+ return label;
+ }
+
+ public void setLabel(String label) {
+ this.label = label;
+ }
+
+ public String getUuid() {
+ return uuid;
+ }
+
+ public void setUuid(String uuid) {
+ this.uuid = uuid;
+ }
+ }
+
+ public class WorkflowStepDTO {
+ @SerializedName("id")
+ private int id;
+
+ @SerializedName("type")
+ private String type;
+
+ @SerializedName("annotation")
+ private String annotation;
+
+ public int getId() {
+ return id;
+ }
+
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ public String getAnnotation() {
+ return annotation;
+ }
+
+ public void setAnnotation(String annotation) {
+ this.annotation = annotation;
+ }
+ }
+
+ public AlgorithmDTO convertToAlgorithmDTO(){
+
+ AlgorithmDTO algorithmDTO = new AlgorithmDTO();
+
+ // Transfer workflow information
+ algorithmDTO.setName(id);
+ algorithmDTO.setDesc("");
+ algorithmDTO.setLabel(name);
+ algorithmDTO.setType("workflow");
+
+ // Transfer workflow parameters information
+ List<AlgorithmDTO.AlgorithmParamDTO> algorithmParams = new LinkedList<>();
+ Gson gson = new Gson();
+ for (Map.Entry<String, WorkflowInputDTO> workflowInput : getInputs().entrySet()) {
+
+ // Convert the annotation to algorithm Parameter
+ AlgorithmDTO.AlgorithmParamDTO algorithmParam;
+ if(steps.get(workflowInput.getKey()).getAnnotation() != null) {
+ algorithmParam = gson.fromJson(steps.get(workflowInput.getKey()).getAnnotation(),
+ AlgorithmDTO.AlgorithmParamDTO.class);
+ }else{
+ // If annotation is not provided, auto-fill some information
+ algorithmParam = new AlgorithmDTO.AlgorithmParamDTO();
+ // When the constraints are not known, set the most relaxed constraints
+ algorithmParam.setDesc("");
+ algorithmParam.setValue("");
+ algorithmParam.setValueType("string");
+ algorithmParam.setValueNotBlank("false");
+ algorithmParam.setDefaultValue("");
+ algorithmParam.setDefaultValue("true");
+ // If label is dataset/pathology/filter/formula the type should be the same
+ if(workflowInput.getValue().getLabel().equals("dataset") ||
+ workflowInput.getValue().getLabel().equals("pathology")||
+ workflowInput.getValue().getLabel().equals("filter")||
+ workflowInput.getValue().getLabel().equals("formula")){
+ algorithmParam.setType(workflowInput.getValue().getLabel());
+ }else if(workflowInput.getValue().getLabel().equals("x") ||
+ workflowInput.getValue().getLabel().equals("y")){
+ algorithmParam.setType("column");
+ algorithmParam.setColumnValuesSQLType("text,real,integer");
+ algorithmParam.setColumnValuesIsCategorical("");
+ }else{
+ algorithmParam.setType("other");
+ }
+ }
+ // Set the name to the workflow id
+ algorithmParam.setName(workflowInput.getValue().getUuid());
+ algorithmParam.setLabel(workflowInput.getValue().getLabel());
+
+ algorithmParams.add(algorithmParam);
+ }
+ algorithmDTO.setParameters(algorithmParams);
+
+ return algorithmDTO;
+ }
+
+}
diff --git a/src/main/java/eu/hbp/mip/utils/JWTUtil.java b/src/main/java/eu/hbp/mip/utils/JWTUtil.java
deleted file mode 100644
index 1e74841842150aef10778726040b88a53d14d218..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/utils/JWTUtil.java
+++ /dev/null
@@ -1,19 +0,0 @@
-package eu.hbp.mip.utils;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import com.auth0.jwt.algorithms.Algorithm;
-import com.auth0.jwt.JWT;
-
-public class JWTUtil {
-
- private static final Logger LOGGER = LoggerFactory.getLogger(JWT.class);
-
- public static String getJWT(String secret, String subject) {
- LOGGER.info("getJWT");
- Algorithm algorithm = Algorithm.HMAC512(secret);
- String token = JWT.create().withIssuer("mip.humanbrainproject.eu").withSubject(subject).sign(algorithm);
-
- return token;
- }
-}
\ No newline at end of file
diff --git a/src/main/java/eu/hbp/mip/utils/UserActionLogging.java b/src/main/java/eu/hbp/mip/utils/UserActionLogging.java
index 745fc24a6ca53951c1f43cd9db2f6fa5965a73d4..b4a96fc864a16063c39dede8ea0233fbfd41b981 100644
--- a/src/main/java/eu/hbp/mip/utils/UserActionLogging.java
+++ b/src/main/java/eu/hbp/mip/utils/UserActionLogging.java
@@ -4,8 +4,6 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.security.core.context.SecurityContextHolder;
-import java.time.LocalTime;
-
public class UserActionLogging {
@@ -13,11 +11,15 @@ public class UserActionLogging {
public static void LogAction(String actionName, String actionIdInfo)
{
- LOGGER.info( LocalTime.now()+" User : "
+ LOGGER.info( " User : "
+ SecurityContextHolder.getContext().getAuthentication().getName()
- + " called enpoint " + actionName
- + " info "
- + actionIdInfo);
+ + " called endpoint: " + actionName
+ + " info: " + actionIdInfo);
}
+ // Used from Threads because LogAction won't work.
+ public static void LogThreadAction(String actionName, String actionIdInfo)
+ {
+ LOGGER.info( "Thread -->" + actionName + " info: " + actionIdInfo);
+ }
}
diff --git a/src/main/resources/db/migration/V6_0__AddWorkflowDetails.sql b/src/main/resources/db/migration/V6_0__AddWorkflowDetails.sql
new file mode 100644
index 0000000000000000000000000000000000000000..0e508b0efda4aa4842ebc9ff52d3b688761aca5b
--- /dev/null
+++ b/src/main/resources/db/migration/V6_0__AddWorkflowDetails.sql
@@ -0,0 +1,2 @@
+ALTER TABLE experiment ADD COLUMN workflowhistoryid text;
+ALTER TABLE experiment ADD COLUMN workflowstatus text;
\ No newline at end of file